Intercompany AP/AR Netting/Offset

Hello, 
If I understand your process well, you would like to close/pay all outstanding intercompany invoices and leave a difference only on separate account. 

I think you can use difference items (let’s say in AP) - after netting close remaining AP or AR items in 0 value mixed payment line adding difference item for outstanding balance (you can create difference item as new line in transaction Matching dialog for supplier or customer payment, checking “new difference item” flag). Difference items have its own posting type (IP20 in AP/IP21 in AR) so you can direct these postings to specific account - and supplier/customer will be identified.

Alternatively, you can use dedicated cash account (PP1 posting control set to intercompany offset account) and mixed payment containing all AP and AR open items instead of netting. In this case it will be difficult to have separate account for each sister company - you would need one cash account per each. 

But is this process really necessary? In one of my past assignments, AP and AR invoices for sister companies were booked from the beginning on dedicated account (IP1/IP2 posting control) and balance of this account was in fact intercompany offset. Supplier and customer group indicated as well sister company code in dedicated (Interco) code part, so individual companies were identified in the balance. But interco invoices there were subject of regular payments there. I am not sure if it is your case as well.